plotDataOverview(MOFA_simple)
# Calculate the variance explained (R2) per factor in each view
r2 <- calculateVarianceExplained(MOFA_simple)
r2$R2Total
## CyTOF_exp RNA_topgenes mutation
## 0.11896905 0.43082302 0.06067289
# Variance explained by each factor in each view
head(r2$R2PerFactor)
## CyTOF_exp RNA_topgenes mutation
## LF1 1.310245e-02 0.10388835 6.019647e-02
## LF2 8.866526e-02 0.04208622 5.061156e-05
## LF3 5.075316e-04 0.09063537 5.523796e-05
## LF4 1.033843e-04 0.05257305 4.547213e-05
## LF5 1.605860e-02 0.02319636 6.661611e-05
## LF6 8.632895e-05 0.03475225 7.062582e-05
# Plot it
plotVarianceExplained(MOFA_simple)
plotWeightsHeatmap(
MOFA_simple,
view = "CyTOF_exp",
factors = 1:5,
show_colnames = FALSE, main = 'CyTOF_exp'
)
plotTopWeights(
MOFA_simple,
view="CyTOF_exp",
factor=2
)
plotTopWeights(
MOFA_simple,
view="CyTOF_exp",
factor=1
)
plotTopWeights(
MOFA_simple,
view="CyTOF_exp",
factor=5
)
plotWeightsHeatmap(
MOFA_simple,
view = "RNA_topgenes",
factors = 1:5,
show_colnames = FALSE, main = 'RNA_topgenes'
)
plotTopWeights(
MOFA_simple,
view="RNA_topgenes",
factor=1
)
plotTopWeights(
MOFA_simple,
view="RNA_topgenes",
factor=2
)
plotTopWeights(
MOFA_simple,
view="RNA_topgenes",
factor=3
)
plotWeightsHeatmap(
MOFA_simple,
view = "mutation",
factors = 1:5,
show_colnames = F, main = 'Mutation Data'
)
plotTopWeights(
MOFA_simple,
view="mutation",
factor=1
)
# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns
# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
MOFA_simple,
view = "RNA_topgenes",
feature.sets = reactomeGS,
alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)
interestingFactors <- 1:2
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 3:4
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 5:6
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "TP53"
)
## Registered S3 method overwritten by 'GGally':
## method from
## +.gg ggplot2
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "KRAS"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "EGFR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "Mye_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "Tc_154Sm_CD45"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "Tc_168Er_CD8"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "Epi_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple,
factors = c(1:5),
color_by = "FMes_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotDataOverview(MOFA_simple2)
# Calculate the variance explained (R2) per factor in each view
r2 <- calculateVarianceExplained(MOFA_simple2)
r2$R2Total
## CyTOF_prcnt RNA_topgenes mutation
## 0.03829975 0.43071879 0.06079154
# Variance explained by each factor in each view
head(r2$R2PerFactor)
## CyTOF_prcnt RNA_topgenes mutation
## LF1 0.0139093571 0.10400881 6.027968e-02
## LF2 0.0009794348 0.09060074 5.498855e-05
## LF3 0.0052959796 0.05252956 4.739019e-05
## LF4 0.0006543602 0.04194804 8.133970e-05
## LF5 0.0022720214 0.03479404 7.135350e-05
## LF6 0.0137766187 0.02318487 6.811659e-05
# Plot it
plotVarianceExplained(MOFA_simple2)
plotWeightsHeatmap(
MOFA_simple2,
view = "CyTOF_prcnt",
factors = 1:6,
show_colnames = FALSE, main = 'CyTOF_prcnt'
)
plotTopWeights(
MOFA_simple2,
view="CyTOF_prcnt",
factor=1
)
plotTopWeights(
MOFA_simple2,
view="CyTOF_prcnt",
factor=3
)
plotTopWeights(
MOFA_simple2,
view="CyTOF_prcnt",
factor=6
)
plotWeightsHeatmap(
MOFA_simple2,
view = "RNA_topgenes",
factors = 1:6,
show_colnames = FALSE, main = 'RNA_topgenes'
)
plotTopWeights(
MOFA_simple2,
view="RNA_topgenes",
factor=1
)
plotTopWeights(
MOFA_simple2,
view="RNA_topgenes",
factor=2
)
plotTopWeights(
MOFA_simple2,
view="RNA_topgenes",
factor=3
)
plotWeightsHeatmap(
MOFA_simple2,
view = "mutation",
factors = 1:6,
show_colnames = F, main = 'Mutation Data'
)
plotTopWeights(
MOFA_simple2,
view="mutation",
factor=1
)
# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns
# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
MOFA_simple2,
view = "RNA_topgenes",
feature.sets = reactomeGS,
alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)
interestingFactors <- 1:2
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple2,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 3:4
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple2,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 5:6
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple2,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "TP53"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "KRAS"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "EGFR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "Epithelial_10"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "Epithelial_1"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "Endothelial"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple2,
factors = c(1:5),
color_by = "Endothelial"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatter(
MOFA_simple2,
factors = 1:2, dot_size = 3,
color_by = "TP53", # color by the IGHV values that are part of the training data
)
plotFactorScatter(
MOFA_simple2,
factors = 1:2, dot_size = 3,
color_by = "ENSG00000060718",
name_color = 'COL11A1'
)
plotFactorScatter(
MOFA_simple2,
factors = 1:2, dot_size = 3,
color_by = "Epithelial_1",
)
plotDataOverview(MOFA_simple3)
# Calculate the variance explained (R2) per factor in each view
r2 <- calculateVarianceExplained(MOFA_simple3)
r2$R2Total
## CyTOF_exp CyTOF_prcnt RNA_topgenes mutation
## 0.12115006 0.06906895 0.43082705 0.06064075
# Variance explained by each factor in each view
head(r2$R2PerFactor)
## CyTOF_exp CyTOF_prcnt RNA_topgenes mutation
## LF1 1.259907e-02 0.0144383661 0.10388770 6.016669e-02
## LF2 8.989940e-02 0.0274677976 0.04209575 4.993764e-05
## LF3 4.733282e-04 0.0009442448 0.09060997 5.514935e-05
## LF4 1.740497e-02 0.0179105781 0.02318013 6.548418e-05
## LF5 1.311077e-04 0.0054420308 0.05259932 4.527307e-05
## LF6 8.860807e-05 0.0017749235 0.03474953 7.050227e-05
# Plot it
plotVarianceExplained(MOFA_simple3)
plotWeightsHeatmap(
MOFA_simple3,
view = "CyTOF_exp",
factors = 1:5,
show_colnames = FALSE, main = 'CyTOF_exp'
)
plotTopWeights(
MOFA_simple3,
view="CyTOF_exp",
factor=2
)
plotTopWeights(
MOFA_simple3,
view="CyTOF_exp",
factor=1
)
plotTopWeights(
MOFA_simple3,
view="CyTOF_exp",
factor=5
)
plotWeightsHeatmap(
MOFA_simple2,
view = "CyTOF_prcnt",
factors = 1:6,
show_colnames = FALSE, main = 'CyTOF_prcnt'
)
plotTopWeights(
MOFA_simple2,
view="CyTOF_prcnt",
factor=1
)
plotTopWeights(
MOFA_simple2,
view="CyTOF_prcnt",
factor=3
)
plotTopWeights(
MOFA_simple2,
view="CyTOF_prcnt",
factor=6
)
plotWeightsHeatmap(
MOFA_simple3,
view = "RNA_topgenes",
factors = 1:5,
show_colnames = FALSE, main = 'RNA_topgenes'
)
plotTopWeights(
MOFA_simple3,
view="RNA_topgenes",
factor=1
)
plotTopWeights(
MOFA_simple3,
view="RNA_topgenes",
factor=2
)
plotTopWeights(
MOFA_simple3,
view="RNA_topgenes",
factor=3
)
plotWeightsHeatmap(
MOFA_simple3,
view = "mutation",
factors = 1:5,
show_colnames = F, main = 'Mutation Data'
)
plotTopWeights(
MOFA_simple3,
view="mutation",
factor=1
)
# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns
# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
MOFA_simple3,
view = "RNA_topgenes",
feature.sets = reactomeGS,
alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)
interestingFactors <- 1:2
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple3,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 3:4
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple3,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 5:6
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple3,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "TP53"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "KRAS"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "EGFR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "Mye_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "Tc_154Sm_CD45"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "Tc_168Er_CD8"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "Epi_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple3,
factors = c(1:5),
color_by = "FMes_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
## Warning: Removed 11 rows containing missing values (geom_point).
plotDataOverview(MOFA_simple4)
# Calculate the variance explained (R2) per factor in each view
r2 <- calculateVarianceExplained(MOFA_simple4)
r2$R2Total
## CyTOF_prcnt RNA_topgenes mutation radiomics
## 0.03798793 0.43249415 0.05016605 0.23203561
# Variance explained by each factor in each view
head(r2$R2PerFactor)
## CyTOF_prcnt RNA_topgenes mutation radiomics
## LF1 0.0101909453 0.10849324 4.969190e-02 3.172252e-02
## LF2 0.0123359808 0.05026874 2.369753e-05 4.889331e-02
## LF3 0.0080378676 0.09005975 8.527804e-05 3.628949e-05
## LF4 0.0023033604 0.03567126 3.388832e-05 4.631124e-02
## LF5 0.0002113700 0.04182733 3.142110e-05 3.510666e-02
## LF6 0.0006335965 0.03026588 2.776464e-05 4.512130e-02
# Plot it
plotVarianceExplained(MOFA_simple4)
plotWeightsHeatmap(
MOFA_simple4,
view = "CyTOF_prcnt",
factors = 1:6,
show_colnames = FALSE, main = 'CyTOF_prcnt'
)
plotTopWeights(
MOFA_simple4,
view="CyTOF_prcnt",
factor=1
)
plotTopWeights(
MOFA_simple4,
view="CyTOF_prcnt",
factor=3
)
plotTopWeights(
MOFA_simple4,
view="CyTOF_prcnt",
factor=6
)
plotWeightsHeatmap(
MOFA_simple4,
view = "RNA_topgenes",
factors = 1:6,
show_colnames = FALSE, main = 'RNA_topgenes'
)
plotTopWeights(
MOFA_simple4,
view="RNA_topgenes",
factor=1
)
plotTopWeights(
MOFA_simple4,
view="RNA_topgenes",
factor=2
)
plotTopWeights(
MOFA_simple4,
view="RNA_topgenes",
factor=3
)
plotWeightsHeatmap(
MOFA_simple4,
view = "mutation",
factors = 1:6,
show_colnames = F, main = 'Mutation Data'
)
plotTopWeights(
MOFA_simple4,
view="mutation",
factor=1
)
plotWeightsHeatmap(
MOFA_simple4,
view = "radiomics",
factors = 1:6,
show_colnames = F, main = 'Radiomics Data'
)
plotTopWeights(
MOFA_simple4,
view="radiomics",
factor=1
)
plotTopWeights(
MOFA_simple4,
view="radiomics",
factor=2
)
# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns
# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
MOFA_simple4,
view = "RNA_topgenes",
feature.sets = reactomeGS,
alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)
interestingFactors <- 1:2
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple2,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 3:4
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple4,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
interestingFactors <- 5:6
fseaplots <- lapply(interestingFactors, function(factor) {
plotEnrichment(
MOFA_simple4,
gsea,
factor = factor,
alpha = 0.01,
max.pathways = 10 # The top number of pathways to display
)
})
cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
ncol = 1, labels = paste("Factor", interestingFactors))
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "TP53"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "KRAS"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "EGFR"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "Epithelial_10"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "Epithelial_1"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "Endothelial"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatters(
MOFA_simple4,
factors = c(1:5),
color_by = "Endothelial"
)
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
## Warning: Removed 15 rows containing missing values (geom_point).
plotFactorScatter(
MOFA_simple4,
factors = 1:2, dot_size = 3,
color_by = "TP53", # color by the IGHV values that are part of the training data
)
plotFactorScatter(
MOFA_simple4,
factors = 1:2, dot_size = 3,
color_by = "ENSG00000060718",
name_color = 'COL11A1'
)
plotFactorScatter(
MOFA_simple4,
factors = 1:2, dot_size = 3,
color_by = "Epithelial_1",
)
plotFactorScatter(
MOFA_simple4,
factors = 1:2, dot_size = 3,
color_by = "SILA_S",
)